Structural (at 100 K) and DFT studies of 2'-nitro-flavone.

The geometry of the title mol-ecule [systematic name: 2-(2-nitro-phen-yl)-4H-chromen-4-one], C15H9NO4, is determined by two dihedral angles formed by the mean plane of phenyl ring with the mean planes of chromone moiety and nitro group, being 50.73 (5) and 30.89 (7)°, respectively. The crystal packing is determined by π-π inter-actions and C-H⋯O contacts. The results of DFT calculations at the B3LYP/6-31G* level of theory provided an explanation of the unusually large dihedral angle between the chromone moiety and the phenyl group. The electrostatic potential map on the mol-ecular surface was calculated in order to determine the potential binding sites to receptors. © Oskolkov et al. 2020.

Chemical context

The naturally occurring group of heterocyclic compounds known as flavonoids has received considerable attention over the past 15 years. The synthesis and applications of flavones and their derivatives have been studied extensively because of their diverse pharmaceutical properties. Besides their physiological role in plants (Agati et al., 2012 ▸), this class of compounds has demonstrated anti­allergic, anti­viral, anxiolytic and anti-inflammatory activities (Manthey et al., 2001 ▸). Several synthetic flavonoids and their nitro derivatives, including a few halogen-substituted compounds, have been found to act as highly competitive ligands for benzodiazepine receptors, suggesting a possible use as anxiolytic drugs (Marder et al., 1995 ▸). Most importantly, several nitro derivatives of flavones have been reported to possess anti­proliferative properties against human and murine cancerous cells, by the mechanism of induced apoptosis (Blank et al., 2004 ▸). Moreover, some flavonoids have been found to be capable of restoring the viability of human vascular endothelial cells, thus providing both cytoprotective and cytotoxic effects on normal and cancerous cells, respectively (Ramos, 2008 ▸). The title compound, 2′-nitro­flavone, has previously been shown to effectively inhibit human and murine tumor cell activity without affecting the non-tumor cells. Induced apoptosis mol­ecular mechanisms have been studied in vitro for HeLa human cervix carcinoma (Cárdenas et al., 2008 ▸) and in vivo in murine adenocarcinoma cells (Cárdenas et al., 2009 ▸). Several haematological cancer cell lines were used in the cytotoxicity evaluation of the title compound, along with a culture of healthy peripheral blood mononuclear cells (PBMCs); the IC50 values (drug concentrations needed to induce a 50% inhibition of cell growth) after 2′-nitro­flavone treatment ranged from 1±0.5 µmol L−1 to 9±1.4 µmol/L for various neoplastic cells, while the healthy cells IC50 was found to be over 80 µmol L−1, effectively leaving the cells intact under the concentrations sufficient for cancerous cells (Cárdenas et al., 2012 ▸). Despite the evident importance of nitro­flavone derivatives, structural studies until now have been limited to only one reported nitro­flavone-based compound (Kendi et al., 1996 ▸). In this work, a combined study consisting of X-ray diffraction (XRD) structural analysis and quantum-chemical DFT calculations was carried out in order to obtain insight into the structure–property relationship, and more specifically the effect of the nitro substituent in the ortho-position of the phenyl moiety of a flavone.

Structural commentary

The mol­ecular structure of 2′-nitro­flavone is presented in Fig. 1 ▸. The mean plane of the benzene ring makes dihedral angles of 50.73 (5) and 30.89 (7)° with the mean planes of the chromone moiety and the nitro group, respectively. The dihedral angle between mean planes of the chromone and benzene groups is unusually large when compared to other ortho-substituted flavone derivatives. For instance, the mol­ecule of 2′-meth­oxy­flavone was reported to be almost planar, with a dihedral angle of 2.9° (Wallet et al., 1990 ▸). Even in the flavonoid with a bulky carbazole substituent in the same position, this dihedral angle is only 29.2° (Zheng, 2018 ▸). The length of the single bond between the chromone and benzene moieties is 1.469 (2) Å, indicating some π–π conjugation. The unusually large dihedral angle in the title mol­ecule can be attributed to the steric tension between the nitro group and the chromone oxygen atom, whereas in the carbazole derivative this substituent is twisted far enough from the plane of the benzene ring to avoid it coming into close proximity with the flavone core.

Figure 1

A view of the mol­ecular structure of the title compound with the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.

Supra­molecular features

In the crystal, the title mol­ecules form a parquet-like structure, with alternating layers of coplanar chromone backbones (Fig. 2 ▸). The presence of π–π inter­actions in the crystal packing can be suggested from the short inter­molecular distance of 3.299 (4) Å between the overlapping C9 atoms from opposing mol­ecules. Moreover, a short contact of 3.286 (3) Å between the carbonyl oxygen atom and the centroid of the opposing heterocyclic ring is found, which suggests an inter­action of the oxygen atom with the π-system (Fig. 3 ▸). Such an inter­molecular inter­action was found in the crystal structure of chiral amino alcohol with a penta­fluoro­phenyl group (Korenaga et al., 2003 ▸). Two short C—H⋯O contacts also occur, indicating at additional structural stability (Table 1 ▸).

Figure 2

Parquet-like mol­ecular packing in the title structure.

Figure 3

Short inter­molecular C⋯C and C—O⋯π contacts in the crystal of the title compound.

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C3—H3⋯O4i	0.933 (17)	2.675 (16)	3.198 (3)	116.1 (12)
C4—H4⋯O4i	0.971 (16)	2.446 (16)	3.109 (3)	125.3 (12)

Symmetry code: (i) .

Database survey

A search of the Cambridge Crystallographic Database (CSD version 5.40, update of September 19; Groom et al., 2016 ▸) for the title mol­ecule yielded no entries. A single nitro­flavone entry, for 2′-methyl-3′-nitro­flavone, was found (REZROD; Kendi et al., 1996 ▸). A search for flavone-core mol­ecules with only an ortho-substituted phenyl ring returned a total of six entries, three of which correspond to the compound with a meth­oxy group in the 2′-position [KEPLAS (Wallet et al., 1990 ▸), KEPLAS01 (McKendall et al., 2008 ▸), KEPLAS02 (Zia et al.., 2020 ▸)]; more specifically, one of the entries represents a structure of a possible polymorph, while the other two correspond to the same form. The other three correspond to carbazole (XIJVAQ; Zheng, 2018 ▸), hy­droxy (YUDWEZ; Seetharaman & Rajan, 1995 ▸) and ethyl glycolate (PIGXUB; Goyal et al., 2018 ▸) substituents. Most of these mol­ecules exhibit only slight deviations from planarity, with the exception of carbazole-substituted mol­ecule.

DFT calculations

In an attempt to get further insight into structure and properties of the title mol­ecule (I), a DFT study was carried out at the B3LYP/6-31G* level of theory with GAUSSIAN 16 (Frisch et al., 2016 ▸) software. The geometry of the ground state was optimized, using the XRD data as a starting point. The optimized geometry was confirmed to be the minimum by vibrational frequency analysis. Two previously described flavonoids, with meth­oxy (II) and carbazole (III) substituents in the 2′-position, were also optimized and compared with the XRD data. Selected geometrical parameters are presented in Tables 2 ▸–4 ▸ ▸.

Table 2

Experimental (XRD) and calculated (DFT) dihedral angles (°) between the phenyl and chromone moieties in the title mol­ecule (I), the 2′-meth­oxy derivative (II) and the 2′-carbazole derivative (III)

	XRD	DFT
(I)	50.73 (5)	47.56
(II)	2.89 (7)	22.16
(III)	29.21 (6)	40.13

Table 3

Experimental (XRD) and calculated (DFT) lengths of single bonds (Å) between the phenyl and chromone moieties in the title mol­ecule (I), the 2′-meth­oxy derivative (II) and the 2′-carbazole derivative (III)

	XRD	DFT
(I)	1.469 (2)	1.482
(II)	1.475 (4)	1.477
(III)	1.478 (2)	1.481

Table 4

Experimental (XRD) and calculated (DFT) dihedral/torsion angles (°) between the phenyl group and the substituent in the 2′-position in the title mol­ecule (I), the meth­oxy derivative (II) and the carbazole derivative (III)

	XRD	DFT
(I)	30.89 (7)	31.83
(II)	174.3 (2)	176.78
(III)	69.95 (9)	66.40

The calculated parameters are in satisfactory agreement with those obtained experimentally. The range of calculated dihedral angles between the moieties comprising the flavone core is narrower than that observed in the crystal structures, but still demonstrates the same trend with the title compound having the largest angle.

Considering the importance of the biological functions of the title compound, including its ability to competitively bind to benzodiazepine receptors, the electrostatic potential on the van der Waals surface was calculated (Fig. 4 ▸). While initially we had expected the nitro group to be the negative charge concentration site, it turned out to be the oxygen of the chromone moiety. We speculate that it could be the binding part in this mol­ecule’s inter­action with benzodiazepine receptors.

Figure 4

Electrostatic potential on the van der Waals surface of the title compound.

Synthesis and crystallization

The synthesis of the title compound was performed as described in the literature (Barros & Silva, 2006 ▸). The obtained product was recrystallized by slow evaporation from ethanol solution.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 5 ▸. Data collection was performed at 100 K. All hydrogen atoms were located from the difference-Fourier map and freely refined.

Table 5

Experimental details

Crystal data
Chemical formula	C15H9NO4
M r	267.23
Crystal system, space group	Monoclinic, P21/c
Temperature (K)	100
a, b, c (Å)	8.079 (7), 20.134 (17), 7.915 (7)
β (°)	116.647 (18)
V (Å3)	1150.6 (16)
Z	4
Radiation type	Mo Kα
μ (mm−1)	0.11
Crystal size (mm)	0.35 × 0.28 × 0.25
Data collection
Diffractometer	Bruker APEXII CCD
No. of measured, independent and observed [I > 2σ(I)] reflections	9944, 2491, 2248
R int	0.034
(sin θ/λ)max (Å−1)	0.650
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S	0.035, 0.093, 1.05
No. of reflections	2491
No. of parameters	217
H-atom treatment	All H-atom parameters refined
Δρmax, Δρmin (e Å−3)	0.30, −0.23

Computer programs: APEX3 and SAINT (Bruker, 2016 ▸), SHELXT2017/1 (Sheldrick, 2015a ▸), SHELXL2017/1 (Sheldrick, 2015b ▸) and Mercury (Macrae et al., 2020 ▸).

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989020010713/yk2138sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989020010713/yk2138Isup3.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S2056989020010713/yk2138Isup3.cml

CCDC reference: 2021153

Additional supporting information: crystallographic information; 3D view; checkCIF report

C15H9NO4	F(000) = 552
Mr = 267.23	Dx = 1.543 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
a = 8.079 (7) Å	Cell parameters from 1326 reflections
b = 20.134 (17) Å	θ = 3.1–32.1°
c = 7.915 (7) Å	µ = 0.11 mm−1
β = 116.647 (18)°	T = 100 K
V = 1150.6 (16) Å3	Block-shaped, white
Z = 4	0.35 × 0.28 × 0.25 mm

Bruker APEXII CCD diffractometer	Rint = 0.034
φ and ω scans	θmax = 27.5°, θmin = 2.0°
9944 measured reflections	h = −10→6
2491 independent reflections	k = −16→26
2248 reflections with I > 2σ(I)	l = −10→8

Refinement on F2	Primary atom site location: iterative
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035	All H-atom parameters refined
wR(F2) = 0.093	w = 1/[σ2(Fo2) + (0.0401P)2 + 0.551P] where P = (Fo2 + 2Fc2)/3
S = 1.05	(Δ/σ)max = 0.001
2491 reflections	Δρmax = 0.30 e Å−3
217 parameters	Δρmin = −0.23 e Å−3
0 restraints

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

	x	y	z	Uiso*/Ueq
O3	0.22049 (12)	0.13047 (4)	0.89731 (12)	0.0160 (2)
O4	0.48862 (13)	−0.02543 (4)	1.23925 (13)	0.0229 (2)
O1	0.04077 (13)	0.29953 (4)	0.98796 (14)	0.0230 (2)
O2	0.11312 (14)	0.20433 (4)	1.12606 (14)	0.0243 (2)
C7	0.37958 (17)	0.13828 (6)	1.06058 (17)	0.0154 (2)
C10	0.22802 (17)	0.01385 (6)	0.96633 (16)	0.0146 (2)
C9	0.40481 (17)	0.02123 (6)	1.13800 (17)	0.0160 (2)
C15	0.14347 (17)	0.06830 (5)	0.85277 (17)	0.0144 (2)
C14	−0.02257 (17)	0.06319 (6)	0.68804 (17)	0.0163 (2)
C2	0.33977 (17)	0.26206 (6)	1.08494 (16)	0.0148 (2)
C13	−0.10846 (18)	0.00246 (6)	0.63791 (17)	0.0182 (3)
C1	0.44677 (17)	0.20715 (6)	1.09092 (16)	0.0154 (2)
N1	0.15066 (15)	0.25441 (5)	1.06335 (14)	0.0164 (2)
C8	0.47167 (18)	0.08861 (6)	1.17707 (17)	0.0175 (3)
C11	0.13820 (18)	−0.04727 (6)	0.91170 (17)	0.0168 (3)
C6	0.62821 (18)	0.21870 (6)	1.12309 (18)	0.0194 (3)
C3	0.40847 (18)	0.32564 (6)	1.10911 (17)	0.0165 (3)
C5	0.69942 (19)	0.28224 (6)	1.14845 (19)	0.0204 (3)
C4	0.58971 (18)	0.33551 (6)	1.14135 (17)	0.0185 (3)
C12	−0.02751 (18)	−0.05292 (6)	0.75091 (18)	0.0186 (3)
H13	−0.221 (2)	−0.0009 (7)	0.527 (2)	0.019 (4)*
H11	0.196 (2)	−0.0854 (7)	0.994 (2)	0.020 (4)*
H8	0.585 (2)	0.0986 (8)	1.292 (2)	0.024 (4)*
H14	−0.071 (2)	0.1017 (8)	0.610 (2)	0.020 (4)*
H3	0.334 (2)	0.3611 (8)	1.110 (2)	0.025 (4)*
H4	0.638 (2)	0.3804 (8)	1.162 (2)	0.025 (4)*
H5	0.825 (2)	0.2894 (7)	1.172 (2)	0.022 (4)*
H12	−0.090 (2)	−0.0948 (8)	0.716 (2)	0.024 (4)*
H6	0.706 (2)	0.1816 (8)	1.128 (2)	0.027 (4)*

	U11	U22	U33	U12	U13	U23
O3	0.0160 (5)	0.0119 (4)	0.0168 (4)	−0.0011 (3)	0.0043 (4)	−0.0001 (3)
O4	0.0205 (5)	0.0164 (4)	0.0244 (5)	0.0012 (3)	0.0034 (4)	0.0050 (3)
O1	0.0174 (5)	0.0199 (4)	0.0291 (5)	0.0041 (3)	0.0083 (4)	0.0014 (4)
O2	0.0265 (5)	0.0205 (4)	0.0309 (5)	−0.0026 (4)	0.0175 (5)	0.0039 (4)
C7	0.0149 (6)	0.0148 (5)	0.0168 (5)	−0.0012 (4)	0.0073 (5)	−0.0026 (4)
C10	0.0151 (6)	0.0138 (5)	0.0166 (5)	0.0006 (4)	0.0086 (5)	−0.0012 (4)
C9	0.0158 (6)	0.0151 (5)	0.0173 (5)	0.0008 (4)	0.0077 (5)	0.0007 (4)
C15	0.0161 (6)	0.0125 (5)	0.0169 (5)	−0.0010 (4)	0.0094 (5)	−0.0021 (4)
C14	0.0164 (6)	0.0163 (5)	0.0164 (5)	0.0021 (4)	0.0076 (5)	0.0005 (4)
C2	0.0150 (6)	0.0162 (5)	0.0132 (5)	−0.0006 (4)	0.0062 (5)	−0.0005 (4)
C13	0.0158 (6)	0.0215 (6)	0.0159 (5)	−0.0023 (5)	0.0059 (5)	−0.0034 (4)
C1	0.0173 (6)	0.0129 (5)	0.0146 (5)	−0.0005 (4)	0.0059 (5)	−0.0006 (4)
N1	0.0174 (5)	0.0156 (5)	0.0162 (5)	0.0000 (4)	0.0076 (4)	−0.0020 (4)
C8	0.0165 (6)	0.0160 (6)	0.0169 (5)	−0.0005 (4)	0.0046 (5)	−0.0014 (4)
C11	0.0191 (6)	0.0139 (5)	0.0195 (6)	0.0006 (4)	0.0106 (5)	−0.0009 (4)
C6	0.0182 (7)	0.0156 (6)	0.0236 (6)	0.0009 (5)	0.0087 (5)	−0.0017 (5)
C3	0.0201 (6)	0.0130 (5)	0.0161 (5)	0.0010 (4)	0.0078 (5)	0.0000 (4)
C5	0.0163 (7)	0.0195 (6)	0.0252 (6)	−0.0023 (5)	0.0092 (5)	−0.0012 (5)
C4	0.0211 (7)	0.0142 (5)	0.0201 (6)	−0.0032 (5)	0.0091 (5)	−0.0012 (4)
C12	0.0215 (7)	0.0157 (5)	0.0209 (6)	−0.0037 (5)	0.0115 (5)	−0.0043 (4)

O3—C7	1.3626 (17)	C2—C3	1.3741 (19)
O3—C15	1.3717 (16)	C13—C12	1.3950 (19)
O4—C9	1.2233 (16)	C1—C6	1.390 (2)
O1—N1	1.2224 (15)	C11—C12	1.377 (2)
O2—N1	1.2208 (15)	C6—C5	1.380 (2)
C7—C1	1.4690 (19)	C3—C4	1.383 (2)
C7—C8	1.3373 (18)	C5—C4	1.3765 (19)
C10—C9	1.4722 (19)	C14—H14	0.958 (15)
C10—C15	1.3877 (18)	C13—H13	0.944 (16)
C10—C11	1.3950 (19)	C11—H11	0.979 (15)
C9—C8	1.4415 (19)	C6—H6	0.964 (17)
C15—C14	1.3932 (19)	C3—H3	0.933 (17)
C14—C13	1.3736 (19)	C5—H5	0.953 (17)
C2—C1	1.3911 (18)	C4—H4	0.971 (16)
C2—N1	1.467 (2)	C12—H12	0.957 (16)
C7—O3—C15	118.38 (9)	C12—C11—C10	120.95 (12)
O3—C7—C1	112.72 (10)	C5—C6—C1	121.21 (12)
C8—C7—O3	124.33 (11)	C2—C3—C4	119.18 (11)
C8—C7—C1	122.86 (12)	C4—C5—C6	119.85 (14)
C15—C10—C9	120.66 (11)	C5—C4—C3	120.30 (12)
C15—C10—C11	117.36 (12)	C11—C12—C13	120.55 (12)
C11—C10—C9	121.98 (11)	C13—C14—H14	121.7 (9)
O4—C9—C10	123.36 (12)	C15—C14—H14	119.2 (9)
O4—C9—C8	122.56 (13)	C14—C13—H13	119.0 (9)
C8—C9—C10	114.08 (10)	C12—C13—H13	121.3 (9)
O3—C15—C10	121.31 (12)	C7—C8—H8	119.2 (9)
O3—C15—C14	116.32 (10)	C9—C8—H8	119.7 (9)
C10—C15—C14	122.37 (11)	C12—C11—H11	121.7 (9)
C13—C14—C15	119.06 (11)	C10—C11—H11	117.3 (9)
C1—C2—N1	121.28 (11)	C5—C6—H6	119.4 (10)
C3—C2—C1	121.98 (13)	C1—C6—H6	119.4 (10)
C3—C2—N1	116.64 (11)	C2—C3—H3	119.6 (10)
C14—C13—C12	119.70 (13)	C4—C3—H3	121.1 (10)
C2—C1—C7	124.49 (12)	C4—C5—H5	119.8 (9)
C6—C1—C7	118.02 (11)	C6—C5—H5	120.4 (9)
C6—C1—C2	117.47 (11)	C5—C4—H4	120.9 (10)
O1—N1—C2	117.98 (11)	C3—C4—H4	118.8 (10)
O2—N1—O1	123.63 (12)	C11—C12—H12	120.5 (9)
O2—N1—C2	118.35 (10)	C13—C12—H12	118.9 (9)
C7—C8—C9	121.12 (12)
O3—C7—C1—C2	52.15 (16)	C2—C1—C6—C5	0.11 (19)
O3—C7—C1—C6	−126.13 (13)	C2—C3—C4—C5	0.21 (18)
O3—C7—C8—C9	−1.1 (2)	C1—C7—C8—C9	−177.40 (11)
O3—C15—C14—C13	−178.69 (11)	C1—C2—N1—O1	−152.23 (12)
O4—C9—C8—C7	178.00 (12)	C1—C2—N1—O2	29.74 (16)
C7—O3—C15—C10	−2.47 (17)	C1—C2—C3—C4	−0.34 (18)
C7—O3—C15—C14	177.77 (10)	C1—C6—C5—C4	−0.2 (2)
C7—C1—C6—C5	178.51 (12)	N1—C2—C1—C7	5.50 (17)
C10—C9—C8—C7	−1.92 (18)	N1—C2—C1—C6	−176.22 (10)
C10—C15—C14—C13	1.55 (19)	N1—C2—C3—C4	176.21 (10)
C10—C11—C12—C13	0.61 (19)	C8—C7—C1—C2	−131.15 (14)
C9—C10—C15—O3	−0.57 (18)	C8—C7—C1—C6	50.57 (18)
C9—C10—C15—C14	179.18 (11)	C11—C10—C9—O4	3.2 (2)
C9—C10—C11—C12	179.73 (11)	C11—C10—C9—C8	−176.84 (11)
C15—O3—C7—C1	−179.96 (10)	C11—C10—C15—O3	178.98 (11)
C15—O3—C7—C8	3.39 (18)	C11—C10—C15—C14	−1.27 (18)
C15—C10—C9—O4	−177.23 (12)	C6—C5—C4—C3	0.07 (19)
C15—C10—C9—C8	2.69 (17)	C3—C2—C1—C7	−178.11 (11)
C15—C10—C11—C12	0.18 (18)	C3—C2—C1—C6	0.18 (18)
C15—C14—C13—C12	−0.71 (19)	C3—C2—N1—O1	31.19 (15)
C14—C13—C12—C11	−0.33 (19)	C3—C2—N1—O2	−146.84 (12)

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···O4i	0.933 (17)	2.675 (16)	3.198 (3)	116.1 (12)
C4—H4···O4i	0.971 (16)	2.446 (16)	3.109 (3)	125.3 (12)